Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 148 of 290
Found at i:47157944 original size:26 final size:26
Alignment explanation
Indices: 47157915--47157969 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
47157905 AGACATAACA
47157915 AAAAGAATAAAA-ATAAAAATAAAAAT
1 AAAAG-ATAAAAGATAAAAATAAAAAT
*
47157941 AAAAGATAAAAGATAAAAATAAAGAT
1 AAAAGATAAAAGATAAAAATAAAAAT
47157967 AAA
1 AAA
47157970 CATAAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (26 bp):
AAAAGATAAAAGATAAAAATAAAAAT
Found at i:47159561 original size:23 final size:22
Alignment explanation
Indices: 47159523--47159599 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 22
47159513 TCAAACCAAT
* *
47159523 AGAATAAAAATAAATAATTAAA
1 AGAATAAAAAAAAATAATGAAA
*
47159545 AGAATAAAAAAATAATAATGACA
1 AGAATAAAAAAA-AATAATGAAA
47159568 AGAATAATAATAAGAACATAAT-AAA
1 AGAATAA-AA-AA-AA-ATAATGAAA
47159593 A-AATAAA
1 AGAATAAA
47159600 GAATAGTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
22 11 0.24
23 16 0.35
24 7 0.15
25 6 0.13
26 6 0.13
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.19
Consensus pattern (22 bp):
AGAATAAAAAAAAATAATGAAA
Found at i:47185926 original size:19 final size:19
Alignment explanation
Indices: 47185902--47185968 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 19
47185892 AAATTTGTAA
47185902 ATAATAATATTTTTAAATT
1 ATAATAATATTTTTAAATT
*
47185921 ATAAT-ATGTTTTTAAATT
1 ATAATAATATTTTTAAATT
*
47185939 AATACA-ATATAATTTTAAAATT
1 -ATA-ATA-AT-ATTTTTAAATT
47185961 ATAATAAT
1 ATAATAAT
47185969 TAGATTTTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
18 12 0.31
19 8 0.21
20 4 0.10
21 6 0.15
22 9 0.23
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (19 bp):
ATAATAATATTTTTAAATT
Found at i:47185934 original size:18 final size:16
Alignment explanation
Indices: 47185894--47185939 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
47185884 AATTTTTTAA
* *
47185894 ATTTGTAAATAATAAT
1 ATTTTTAAATTATAAT
47185910 ATTTTTAAATTATAAT
1 ATTTTTAAATTATAAT
47185926 ATGTTTTTAAATTA
1 A--TTTTTAAATTA
47185940 ATACAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 15 0.58
18 11 0.42
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (16 bp):
ATTTTTAAATTATAAT
Found at i:47189275 original size:12 final size:12
Alignment explanation
Indices: 47189255--47189358 Score: 53
Period size: 12 Copynumber: 9.0 Consensus size: 12
47189245 TATTTATCTA
*
47189255 TAAAATAAATAT
1 TAAATTAAATAT
47189267 TAAATTAAAT-T
1 TAAATTAAATAT
*
47189278 TAATATTAAGATAA
1 TAA-ATTAA-ATAT
* * *
47189292 TCACTTTAATAT
1 TAAATTAAATAT
47189304 TAAATT-AATA-
1 TAAATTAAATAT
*
47189314 -AAA-T-ACTAT
1 TAAATTAAATAT
*
47189323 TAAGA-TAAGTAT
1 TAA-ATTAAATAT
47189335 TAAATTAAAT-T
1 TAAATTAAATAT
47189346 TAATATTAAATAT
1 TAA-ATTAAATAT
47189359 ATTAAAATAA
Statistics
Matches: 71, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
8 4 0.06
9 3 0.04
10 2 0.03
11 15 0.21
12 39 0.55
13 6 0.08
14 2 0.03
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (12 bp):
TAAATTAAATAT
Found at i:47189312 original size:20 final size:18
Alignment explanation
Indices: 47189262--47189356 Score: 64
Period size: 17 Copynumber: 5.6 Consensus size: 18
47189252 CTATAAAATA
47189262 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
47189279 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
*
47189299 AATATTAAATTAATA--A
1 AATATTAAATTAATATTT
* *
47189315 AATACT--ATTAAGA--T
1 AATATTAAATTAATATTT
47189329 AAGTATTAAATTAA-ATTT
1 AA-TATTAAATTAATATTT
47189347 AATATTAAAT
1 AATATTAAAT
47189357 ATATTAAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 8 0.13
15 3 0.05
16 6 0.10
17 24 0.38
18 4 0.06
19 3 0.05
20 15 0.24
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:47192443 original size:395 final size:396
Alignment explanation
Indices: 47191665--47192455 Score: 1151
Period size: 395 Copynumber: 2.0 Consensus size: 396
47191655 GCCATAAGGG
* * *
47191665 CATTGATGTATCTTGCAAACAACACAAGACTTGATATAGCTTTCACTATAAACTTATTAGTAAGG
1 CATTGATGTATCTTGCAAACAACACAAGACCTGATATAGCTTTCACTATAAACTTATTAGCAAGA
* * * ** * * *
47191730 TTTAGTTTTTCTCCGACACGTAGACATTAAAATGCATTGACTCAAAGATGTAATGTGATGTTGTT
66 TTTAGTTATTCTCCAACACGTAGACATTAAAACGCATCAACTCAAAGATATAATGTAATATTGTT
** *
47191795 ATTAAGGGGAGTCAAATACACGTTGCACTCTTTTTATTTAACCAAGGTTTTGTCCCACTGGGTTT
131 ATTAAGAAGAGTCAAACACACGTTGCACTCTTTTTATTTAACCAAGGTTTTGTCCCACTGGGTTT
* *
47191860 TCCTGGTAAAAGATTTTAACGAGACAACTTGTAATTGGAGATTTTGAACTCTTTTTCCTTCATTA
196 TCCTGGTAAAAGATTTTAACGAGACAACTTGTAATAGGAGATTTTGAAATCTTTTTCCTTCATTA
* * * *
47191925 GGTTTTTATCCCACATGGTTTTTCTTAATAAGGTTTTAATGAGGCACACTTTCATTGATGGACAT
261 GGTTTTTAGCCCACATGGTTTTTCCTAATAAGGTTTTAACGAGACACACTTTCATTGATGGACAT
* * *
47191990 CCAAGAGGAGTGTTGTAAAATGAATATCTATATAACTCCCATAACCCTGAATAATTCATTTTCTT
326 CCAAGAGGAGTGTTGCAAAATGAATATCCATATAACTCCCATAACCCTGAAGAATTCATTTTCTT
47192055 GTAACT
391 GTAACT
* * * *
47192061 CATTGATGTAT-TGTGCAAACAACACAAGACCTGCTATAGCTTTCATTGTAAACTTGTTAGCAAG
1 CATTGATGTATCT-TGCAAACAACACAAGACCTGATATAGCTTTCACTATAAACTTATTAGCAAG
** * *
47192125 ATTTAGTTATTCTCCAACGTGTAGACATTAGAACGCGTCAACTCAAAGATATAATGTAATATTGT
65 ATTTAGTTATTCTCCAACACGTAGACATTAAAACGCATCAACTCAAAGATATAATGTAATATTGT
** *
47192190 TATTAAGAAGAGTCAAACATGCGTTGCACTC-TTTTATTTAACCAAGGTTTTGTCCCACTGTGTT
130 TATTAAGAAGAGTCAAACACACGTTGCACTCTTTTTATTTAACCAAGGTTTTGTCCCACTGGGTT
*
47192254 TTCCTGGTAAAGGATTTTAACGAGACAACTTGTAATAGGAGATTTTGAAAT-TTTTTCCTTCATT
195 TTCCTGGTAAAAGATTTTAACGAGACAACTTGTAATAGGAGATTTTGAAATCTTTTTCCTTCATT
* *
47192318 AGGTTTTTAGCCCACATGGTTTTTCCTAATAAGGTTTTAACGAGACACGCTTTCATTGATGGGCA
260 AGGTTTTTAGCCCACATGGTTTTTCCTAATAAGGTTTTAACGAGACACACTTTCATTGATGGACA
* * *
47192383 TCCAATGAGGAGTGTTGCAAAAT-AGATGTCCATATAACTCTCATAA-TCTCGAAGAATTCATTT
325 TCCAA-GAGGAGTGTTGCAAAATGA-ATATCCATATAACTCCCATAACCCT-GAAGAATTCATTT
47192446 TCTTGTAACT
387 TCTTGTAACT
47192456 TTTATAACCC
Statistics
Matches: 351, Mismatches: 40, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
394 80 0.23
395 137 0.39
396 134 0.38
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (396 bp):
CATTGATGTATCTTGCAAACAACACAAGACCTGATATAGCTTTCACTATAAACTTATTAGCAAGA
TTTAGTTATTCTCCAACACGTAGACATTAAAACGCATCAACTCAAAGATATAATGTAATATTGTT
ATTAAGAAGAGTCAAACACACGTTGCACTCTTTTTATTTAACCAAGGTTTTGTCCCACTGGGTTT
TCCTGGTAAAAGATTTTAACGAGACAACTTGTAATAGGAGATTTTGAAATCTTTTTCCTTCATTA
GGTTTTTAGCCCACATGGTTTTTCCTAATAAGGTTTTAACGAGACACACTTTCATTGATGGACAT
CCAAGAGGAGTGTTGCAAAATGAATATCCATATAACTCCCATAACCCTGAAGAATTCATTTTCTT
GTAACT
Found at i:47192993 original size:10 final size:10
Alignment explanation
Indices: 47192974--47193050 Score: 66
Period size: 10 Copynumber: 7.6 Consensus size: 10
47192964 AATCTTGAGA
*
47192974 GAGAGGGGGG
1 GAGAGAGGGG
47192984 GAGAGAGGGG
1 GAGAGAGGGG
* *
47192994 GGGTGAGGGAG
1 GAGAGAGGG-G
*
47193005 G-GAGAGGGA
1 GAGAGAGGGG
*
47193014 GAGAGAGGAAG
1 GAGAGAGG-GG
* *
47193025 GAGGGAGGGA
1 GAGAGAGGGG
47193035 GAGAGAGGGG
1 GAGAGAGGGG
47193045 GAGAGA
1 GAGAGA
47193051 TGGATAGAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
9 1 0.02
10 42 0.81
11 9 0.17
ACGTcount: A:0.31, C:0.00, G:0.68, T:0.01
Consensus pattern (10 bp):
GAGAGAGGGG
Found at i:47193086 original size:10 final size:10
Alignment explanation
Indices: 47193071--47193117 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
47193061 AGGAAAGCGG
47193071 GAGAGGGAGA
1 GAGAGGGAGA
47193081 GAGAGGGAG-
1 GAGAGGGAGA
47193090 G-GAGGG-G-
1 GAGAGGGAGA
47193097 GAGAGGGAGA
1 GAGAGGGAGA
47193107 GTA-AGGGAGA
1 G-AGAGGGAGA
47193117 G
1 G
47193118 GGTGGAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
7 2 0.06
8 10 0.30
9 2 0.06
10 18 0.55
11 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.64, T:0.02
Consensus pattern (10 bp):
GAGAGGGAGA
Found at i:47193127 original size:26 final size:25
Alignment explanation
Indices: 47193069--47193129 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
47193059 ATAGGAAAGC
47193069 GGGAGAGGGAGAGAGAGGGAGGGAGG
1 GGGAGAGGGAGAGAGAGGGA-GGAGG
47193095 GGGAGAGGGAGAGTA-AGGGA-GAGG
1 GGGAGAGGGAGAG-AGAGGGAGGAGG
47193119 GTGGAAGAGGG
1 G-GG-AGAGGG
47193130 GGGAAGGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.16
25 2 0.06
26 24 0.75
27 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.66, T:0.03
Consensus pattern (25 bp):
GGGAGAGGGAGAGAGAGGGAGGAGG
Found at i:47193378 original size:35 final size:35
Alignment explanation
Indices: 47193339--47193410 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
47193329 CACCAATATT
47193339 TAAAATTTGGAAAAA-GAAAAAATACTTAGAAATTG
1 TAAAATTT-GAAAAACGAAAAAATACTTAGAAATTG
* *
47193374 TAAAATTTGAAAAACTAAAAGATACTTAGAAATTG
1 TAAAATTTGAAAAACGAAAAAATACTTAGAAATTG
47193409 TA
1 TA
47193411 TAAGTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 6 0.18
35 28 0.82
ACGTcount: A:0.56, C:0.04, G:0.12, T:0.28
Consensus pattern (35 bp):
TAAAATTTGAAAAACGAAAAAATACTTAGAAATTG
Found at i:47204778 original size:61 final size:61
Alignment explanation
Indices: 47204683--47204805 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
47204673 TATGCAATTA
47204683 ACTGTTAAATGTGCATGGTAAGTTAGTGAATTGAAATGTATAAACCTACTAAATATTTTTT
1 ACTGTTAAATGTGCATGGTAAGTTAGTGAATTGAAATGTATAAACCTACTAAATATTTTTT
47204744 ACTGTTAAATGTGCATGGTAAGTTAGTGAATTGAAATGTATAAACCTACTAAATATTTTTT
1 ACTGTTAAATGTGCATGGTAAGTTAGTGAATTGAAATGTATAAACCTACTAAATATTTTTT
47204805 A
1 A
47204806 TACTTATTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (61 bp):
ACTGTTAAATGTGCATGGTAAGTTAGTGAATTGAAATGTATAAACCTACTAAATATTTTTT
Found at i:47214113 original size:19 final size:19
Alignment explanation
Indices: 47214077--47214147 Score: 53
Period size: 18 Copynumber: 3.8 Consensus size: 19
47214067 GCACTAGGTG
*
47214077 ACGTTTTGAAAATTAATAA
1 ACGTTTTGAAAATGAATAA
47214096 ACGTTTTGAAAGA-GAAT-A
1 ACGTTTTGAAA-ATGAATAA
*
47214114 AC--TTTGTAATAATGAAT-T
1 ACGTTTTG-AA-AATGAATAA
*
47214132 ACATTTTGAAAATGAA
1 ACGTTTTGAAAATGAA
47214148 CGACATGTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
16 4 0.09
17 3 0.07
18 16 0.36
19 16 0.36
20 5 0.11
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (19 bp):
ACGTTTTGAAAATGAATAA
Found at i:47214839 original size:6 final size:6
Alignment explanation
Indices: 47214828--47214853 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
47214818 ATTACAGGGA
47214828 CTGGGT CTGGGT CTGGGT CTGGGT CT
1 CTGGGT CTGGGT CTGGGT CTGGGT CT
47214854 CATGATCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.46, T:0.35
Consensus pattern (6 bp):
CTGGGT
Found at i:47226848 original size:44 final size:44
Alignment explanation
Indices: 47226698--47226850 Score: 148
Period size: 47 Copynumber: 3.3 Consensus size: 44
47226688 AAACTGAGTA
* ** * *
47226698 TCTGGGACATGGCATCGGCGTAGAGATGAGTGCCAATGTAAGACGTG
1 TCTGGGACAT-GCATCGGC-TA-AGCTTCGTGCCAGTGTAAGACATG
* *
47226745 TCTGGGACATGCATCAGC-CA-CATTACGATAGCCAGTGTAAGACCATG
1 TCTGGGACATGCATCGGCTAAGC-TT-CG-T-GCCAGTGTAAGA-CATG
*
47226792 TCTGGGACATGCATCGGCTAAGCTTCGTGCCAGTATAAGACATG
1 TCTGGGACATGCATCGGCTAAGCTTCGTGCCAGTGTAAGACATG
47226836 TCTGGGACATGCATC
1 TCTGGGACATGCATC
47226851 AGCACTTATA
Statistics
Matches: 89, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
43 2 0.02
44 20 0.22
45 12 0.13
46 19 0.21
47 32 0.36
48 3 0.03
49 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (44 bp):
TCTGGGACATGCATCGGCTAAGCTTCGTGCCAGTGTAAGACATG
Found at i:47226895 original size:93 final size:94
Alignment explanation
Indices: 47226696--47226949 Score: 275
Period size: 93 Copynumber: 2.7 Consensus size: 94
47226686 TTAAACTGAG
* *
47226696 TATCTGGGACATGGCATCGGCGTAGAGATGAGTGCCAATGTAAGACGTGTCTGGGACATGCATCA
1 TATCTGGGACATGGCATCGGCGTAGAGATGAGTGCCAATATAAGACATGTCTGGGACATGCATCA
* *
47226761 GCCACATTACGATAGCCAGTGTAAGACCA
66 GCCACATCACGAGAGCCAGTGTAAGACCA
* * ** *
47226790 TGTCTGGGACAT-GCATCGGC-TA-AGCTTCGTGCCAGTATAAGACATGTCTGGGACATGCATCA
1 TATCTGGGACATGGCATCGGCGTAGAGATGAGTGCCAATATAAGACATGTCTGGGACATGCATCA
*
47226852 G-CACTTATACACGAGAGCTAGTGTAAGACCA
66 GCCAC--AT-CACGAGAGCCAGTGTAAGACCA
* * * * *
47226883 TATCTGGGACATGGCATCGGCCTCGATGAAGA-TAGCCAGTGTAAGACCATGTCTGGGACATGGC
1 TATCTGGGACATGGCATCGGCGTAGA-GATGAGT-GCCAATATAAGA-CATGTCTGGGACAT-GC
47226947 ATC
62 ATC
47226950 GACAACTTAA
Statistics
Matches: 133, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
90 3 0.02
91 35 0.26
92 4 0.03
93 38 0.29
94 19 0.14
95 1 0.01
96 2 0.02
97 12 0.09
98 14 0.11
99 5 0.04
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (94 bp):
TATCTGGGACATGGCATCGGCGTAGAGATGAGTGCCAATATAAGACATGTCTGGGACATGCATCA
GCCACATCACGAGAGCCAGTGTAAGACCA
Found at i:47226924 original size:49 final size:47
Alignment explanation
Indices: 47226698--47226950 Score: 198
Period size: 49 Copynumber: 5.3 Consensus size: 47
47226688 AAACTGAGTA
* * * * *
47226698 TCTGGGACATGGCATCGGCGTAGAGATGAGT-GCCAATGTAAGA-CGTG
1 TCTGGGACAT-GCATCGGCCTAGATAAGA-TAGCCAGTGTAAGACCATG
* * *
47226745 TCTGGGACATGCATCAGCC-ACATTACGATAGCCAGTGTAAGACCATG
1 TCTGGGACATGCATCGGCCTAGA-TAAGATAGCCAGTGTAAGACCATG
* ** *
47226792 TCTGGGACATGCATCGG-CTAAGCTTCG-T-GCCAGTATAAGA-CATG
1 TCTGGGACATGCATCGGCCT-AGATAAGATAGCCAGTGTAAGACCATG
* * * * *
47226836 TCTGGGACATGCATCAGCACT-TATACACGAGAGCTAGTGTAAGACCATA
1 TCTGGGACATGCATCGGC-CTAGATA-A-GATAGCCAGTGTAAGACCATG
*
47226885 TCTGGGACATGGCATCGGCCTCGATGAAGATAGCCAGTGTAAGACCATG
1 TCTGGGACAT-GCATCGGCCTAGAT-AAGATAGCCAGTGTAAGACCATG
47226934 TCTGGGACATGGCATCG
1 TCTGGGACAT-GCATCG
47226951 ACAACTTAAC
Statistics
Matches: 165, Mismatches: 26, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
44 21 0.13
45 14 0.08
46 26 0.16
47 32 0.19
48 11 0.07
49 50 0.30
50 10 0.06
51 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.22
Consensus pattern (47 bp):
TCTGGGACATGCATCGGCCTAGATAAGATAGCCAGTGTAAGACCATG
Found at i:47231783 original size:19 final size:20
Alignment explanation
Indices: 47231759--47231796 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
47231749 ATAATACCCA
47231759 CCATATC-AAATTTTCAAAG
1 CCATATCAAAATTTTCAAAG
47231778 CCATATCAAAATTTTCAAA
1 CCATATCAAAATTTTCAAA
47231797 CATAAATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.32
Consensus pattern (20 bp):
CCATATCAAAATTTTCAAAG
Found at i:47234502 original size:24 final size:24
Alignment explanation
Indices: 47234470--47234515 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
47234460 CATTGGAGGT
47234470 TTAGATTTGTACATAAATCTCTCA
1 TTAGATTTGTACATAAATCTCTCA
47234494 TTAGATTTGTACATAAATCTCT
1 TTAGATTTGTACATAAATCTCT
47234516 TGGTAAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (24 bp):
TTAGATTTGTACATAAATCTCTCA
Found at i:47236154 original size:80 final size:78
Alignment explanation
Indices: 47236070--47236241 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 78
47236060 GGACTAAGAT
*
47236070 CCGAAGGCATTTGTGCGAG-A-TACAAGTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATAC
1 CCGAAGGCATTTGTGCGAGCATTA-AA--TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATAC
* *
47236133 TAAATCCGGGTTAAGTC
62 TAAAACCGGGCTAAGTC
* * * *
47236150 CCGAAGGCATTCGTGCGAGTCATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAG-CATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
47236215 AACCGGGCTATGTC
65 AACCGGGCTAAGTC
47236229 CCGAAGGCATTTG
1 CCGAAGGCATTTG
47236242 AACGAGGAGC
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
79 38 0.47
80 37 0.46
82 3 0.04
83 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGCATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
ACCGGGCTAAGTC
Found at i:47236232 original size:39 final size:39
Alignment explanation
Indices: 47236017--47236239 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
47236007 TTGAATGCTG
* * * * * *
47236017 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
47236057 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
47236097 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
* *
47236137 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
47236177 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
47236216 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
47236240 TGAACGAGGA
Statistics
Matches: 152, Mismatches: 24, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
39 37 0.24
40 105 0.69
41 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:47236259 original size:79 final size:80
Alignment explanation
Indices: 47236097--47236274 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
47236087 AGATACAAGT
* * * *
47236097 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
47236162 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* * * *
47236177 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* *
47236241 GAACGAG-GAGCTATA
66 GAACGAGTCA-CTAAA
*
47236256 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
47236275 TATGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Found at i:47243672 original size:80 final size:78
Alignment explanation
Indices: 47243588--47243757 Score: 209
Period size: 79 Copynumber: 2.1 Consensus size: 78
47243578 ACTAAGATCA
*
47243588 GAAGGCATTTGTGCGAG-A-TACAAGTTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTA
1 GAAGGCATTTGTGCGAGCATTA-AA--TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTA
* *
47243651 AATCCGGGTTAAGTCCC
62 AAACCGGGCTAAGTCCC
* * * *
47243668 GAAGGCATTCGTGCGAGTCATTAAATCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAA
1 GAAGGCATTTGTGCGAG-CATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAAA
*
47243733 CCGGGCTATGTCCC
65 CCGGGCTAAGTCCC
47243747 GAAGGCATTTG
1 GAAGGCATTTG
47243758 AACGAGGAGC
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
79 38 0.49
80 35 0.45
82 3 0.04
83 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (78 bp):
GAAGGCATTTGTGCGAGCATTAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAAAC
CGGGCTAAGTCCC
Found at i:47243693 original size:40 final size:38
Alignment explanation
Indices: 47243533--47243790 Score: 191
Period size: 40 Copynumber: 6.5 Consensus size: 38
47243523 TTGAATGCTG
* * * * *
47243533 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGT-ACTAAA
** * *
47243573 TCCGGACTAAGAT-CAGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAG-TACTAA-A
* *
47243613 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAG-TACTAAA
*
47243653 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGT-ACTAAA
*
47243693 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAG-TACTAAA
* * * * *
47243732 ACCGGGCTATGTCCCGAAGGCATT-TGAACGAGGAGCTATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTG--CGAGTA-CTAAA
*
47243772 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
47243791 TATGTGATTT
Statistics
Matches: 177, Mismatches: 28, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
38 2 0.01
39 51 0.29
40 113 0.64
41 11 0.06
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (38 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTACTAAA
Found at i:47243748 original size:39 final size:39
Alignment explanation
Indices: 47243533--47243755 Score: 198
Period size: 40 Copynumber: 5.6 Consensus size: 39
47243523 TTGAATGCTG
* * * * * *
47243533 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * * *
47243573 TCCGGACTAAGAT-CAGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
47243613 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
* *
47243653 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
47243693 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
47243732 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
47243756 TGAACGAGGA
Statistics
Matches: 150, Mismatches: 26, Indels: 15
0.79 0.14 0.08
Matches are distributed among these distances:
39 37 0.25
40 103 0.69
41 10 0.07
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:47243775 original size:79 final size:80
Alignment explanation
Indices: 47243613--47243790 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
47243603 AGATACAAGT
* * * *
47243613 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** *
47243678 GTGCGAGTCATTAAA
66 GAACGAGTCACTAAA
* * * *
47243693 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* *
47243757 GAACGAG-GAGCTATA
66 GAACGAGTCA-CTAAA
*
47243772 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
47243791 TATGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTCACTAAA
Found at i:47246960 original size:41 final size:39
Alignment explanation
Indices: 47246901--47247003 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 39
47246891 GAGCTTGGTC
47246901 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCAAACTTAGTT
1 TCGAAGGGC-TTTGAGCCAGTG-TAATAACCAAACTTAGTT
* * **
47246942 TCGAAGGGCTTTAAAGCCAGTGTCATAACCGGACTTAGTT
1 TCGAAGGGCTTT-GAGCCAGTGTAATAACCAAACTTAGTT
*
47246982 CCGAAGGGCCTTTGAGCCAGTG
1 TCGAAGGG-CTTTGAGCCAGTG
47247004 GTCTAATTCG
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
40 33 0.61
41 21 0.39
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (39 bp):
TCGAAGGGCTTTGAGCCAGTGTAATAACCAAACTTAGTT
Found at i:47247060 original size:41 final size:41
Alignment explanation
Indices: 47246891--47247048 Score: 155
Period size: 41 Copynumber: 3.9 Consensus size: 41
47246881 GTCTAAATCT
47246891 GAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAACC
1 GAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAACC
* * * * ** *
47246932 AAACTTAGTTTCGAAGGGCTTTAAAGCCAGTG-TCATAACC
1 GAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAACC
* * *
47246972 G-GACTTAGT-TCCGAAGGGCCTTTGAGCCAGTGGTCTAAT--TC
1 GAG-CTTGGTCT-CGAAGGGCTTTTGAGCCAGT-G-CTAATAACC
47247013 GAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAA
1 GAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAA
47247049 GAATCGGGCT
Statistics
Matches: 94, Mismatches: 16, Indels: 16
0.75 0.13 0.13
Matches are distributed among these distances:
39 5 0.05
40 31 0.33
41 53 0.56
42 2 0.02
43 3 0.03
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (41 bp):
GAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGCTAATAACC
Found at i:47260470 original size:26 final size:26
Alignment explanation
Indices: 47260432--47260481 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
47260422 TATTTTTTGA
47260432 AAATTTTATAATTTTT-TAGAAAATAT
1 AAATTTTATAATTTTTATA-AAAATAT
47260458 AAATTTTGA-AATTTTTATAAAAAT
1 AAATTTT-ATAATTTTTATAAAAAT
47260482 TTTGAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (26 bp):
AAATTTTATAATTTTTATAAAAATAT
Found at i:47266981 original size:41 final size:41
Alignment explanation
Indices: 47266924--47267003 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
47266914 TTTGTTAGAA
47266924 TGAACTGCAGTTTACTATTTTGTATTTTGGGTAGTCTTTAT
1 TGAACTGCAGTTTACTATTTTGTATTTTGGGTAGTCTTTAT
47266965 TGAACTGCAGTTTACTATTTTGTATTTTGGGTAGTCTTT
1 TGAACTGCAGTTTACTATTTTGTATTTTGGGTAGTCTTT
47267004 GTGGCCGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.19, C:0.10, G:0.20, T:0.51
Consensus pattern (41 bp):
TGAACTGCAGTTTACTATTTTGTATTTTGGGTAGTCTTTAT
Found at i:47286012 original size:28 final size:27
Alignment explanation
Indices: 47285954--47286014 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
47285944 TATTTCTTTA
* *
47285954 AATTTACAAAAAAAGACTTATAAGGCC
1 AATTTAAAAAAAAAGACATATAAGGCC
* * *
47285981 AATTTAAAAAATAAAGGCATATATGGCT
1 AATTTAAAAAA-AAAGACATATAAGGCC
47286009 AATTTA
1 AATTTA
47286015 GCCCAAAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 10 0.36
28 18 0.64
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.28
Consensus pattern (27 bp):
AATTTAAAAAAAAAGACATATAAGGCC
Found at i:47289752 original size:44 final size:44
Alignment explanation
Indices: 47289689--47289778 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
47289679 TCTAATAAGC
47289689 CTATACCAATTATATTGTTTGTCACCCTTAGCTAAGAATATTCT
1 CTATACCAATTATATTGTTTGTCACCCTTAGCTAAGAATATTCT
47289733 CTATACCAATTATATTGTTTGTCACCCTTAGCTAAGAATATTCT
1 CTATACCAATTATATTGTTTGTCACCCTTAGCTAAGAATATTCT
47289777 CT
1 CT
47289779 CGGTCTCATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (44 bp):
CTATACCAATTATATTGTTTGTCACCCTTAGCTAAGAATATTCT
Found at i:47299931 original size:19 final size:20
Alignment explanation
Indices: 47299888--47299936 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
47299878 AAATTACAAA
*
47299888 AAAAATAGTTTTCAAACATT
1 AAAAATATTTTTCAAACATT
* *
47299908 TAAAATATTTTTTAAA-ATT
1 AAAAATATTTTTCAAACATT
47299927 AAAAATATTT
1 AAAAATATTT
47299937 ATAAAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (20 bp):
AAAAATATTTTTCAAACATT
Found at i:47299943 original size:19 final size:19
Alignment explanation
Indices: 47299909--47299945 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
47299899 TCAAACATTT
* *
47299909 AAAATATTTTTTAAAATTA
1 AAAATATTTATAAAAATTA
47299928 AAAATATTTATAAAAATT
1 AAAATATTTATAAAAATT
47299946 TTAAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATATTTATAAAAATTA
Found at i:47299976 original size:24 final size:24
Alignment explanation
Indices: 47299934--47299982 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
47299924 ATTAAAAATA
* *
47299934 TTTATAAAAATTTTAAAATTTATTT
1 TTTAGAAAAATTATAAAATTT-TTT
47299959 TTTAGAAAAATTAT-AAATTTTTT
1 TTTAGAAAAATTATAAAATTTTTT
47299982 T
1 T
47299983 CTAAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 6 0.27
25 12 0.55
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTAGAAAAATTATAAAATTTTTT
Found at i:47303618 original size:21 final size:22
Alignment explanation
Indices: 47303592--47303638 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
47303582 CTCTGCTCAA
*
47303592 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
47303613 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
47303635 ACTC
1 ACTC
47303639 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:47309046 original size:14 final size:13
Alignment explanation
Indices: 47309009--47309048 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
47308999 AAACTGTATA
47309009 GTATTTTTGTAAT
1 GTATTTTTGTAAT
*
47309022 GAAATTTTTGTAAT
1 G-TATTTTTGTAAT
47309036 GTATTTATTGTAA
1 GTATTT-TTGTAA
47309049 AATTTATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (13 bp):
GTATTTTTGTAAT
Found at i:47312614 original size:25 final size:25
Alignment explanation
Indices: 47312568--47312616 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
47312558 TTGTTTTTAA
*
47312568 TAGTATATCTTGAAACTGCTATAGG
1 TAGTATATCTTGAAACTACTATAGG
* * *
47312593 TAGTATATGTTGAGATTACTATAG
1 TAGTATATCTTGAAACTACTATAG
47312617 ATAGACTGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
TAGTATATCTTGAAACTACTATAGG
Found at i:47315538 original size:21 final size:21
Alignment explanation
Indices: 47315512--47315561 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
47315502 TCAGCTTAAG
47315512 ACACATGAGACAAATTATCCA
1 ACACATGAGACAAATTATCCA
**
47315533 ACACATGAGGTAAATTATCCA
1 ACACATGAGACAAATTATCCA
*
47315554 ACGCATGA
1 ACACATGA
47315562 CTTGGAGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.20
Consensus pattern (21 bp):
ACACATGAGACAAATTATCCA
Found at i:47320820 original size:48 final size:48
Alignment explanation
Indices: 47320768--47320861 Score: 125
Period size: 48 Copynumber: 2.0 Consensus size: 48
47320758 ATTGAAATTT
* ** * *
47320768 ATTGCAACACTAGAACTTGGAATAAACTTTATAATTTAAATTAGATGA
1 ATTGCAACACTAAAACGAGGAAGAAACTTTATAATATAAATTAGATGA
* *
47320816 ATTGCAACATTAAAACGAGGAAGAAACTTTGTAATATAAATTAGAT
1 ATTGCAACACTAAAACGAGGAAGAAACTTTATAATATAAATTAGAT
47320862 ACATTAGAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.31
Consensus pattern (48 bp):
ATTGCAACACTAAAACGAGGAAGAAACTTTATAATATAAATTAGATGA
Found at i:47326473 original size:6 final size:6
Alignment explanation
Indices: 47326458--47326496 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
47326448 AAGGTGGGTT
*
47326458 TATATA TATATC TATATC TATATC TATATC TATATC TAT
1 TATATC TATATC TATATC TATATC TATATC TATATC TAT
47326497 CCGTGTGGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (6 bp):
TATATC
Found at i:47327611 original size:18 final size:18
Alignment explanation
Indices: 47327568--47327611 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
47327558 GCAAGGGTTG
47327568 CAAGTGCAGTTATCTCCA
1 CAAGTGCAGTTATCTCCA
**
47327586 CATTTGCAGTTATCTCCA
1 CAAGTGCAGTTATCTCCA
47327604 CAAGTGCA
1 CAAGTGCA
47327612 ATTAACAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (18 bp):
CAAGTGCAGTTATCTCCA
Found at i:47336263 original size:46 final size:46
Alignment explanation
Indices: 47336213--47336569 Score: 534
Period size: 46 Copynumber: 7.7 Consensus size: 46
47336203 CTATGATAGA
*
47336213 AAATGTGTAAGACTATGGTTGAAAGATACCATGGCAACCTGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
47336259 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
*
47336305 AAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
*
47336351 AAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
* * *
47336397 AAACGTGTAAGACCATGGTTGAAAGATACCATAGCAACCTGACATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
* ***
47336443 AAATGTGTAAGAACATGGTTGAAAGATACCATGGCAACCTGACGGGG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA-TATG
** * ***
47336490 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACGGGG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA-TATG
**
47336537 AAATGAATAAGACCATGGTTGAAAGATACCATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATG
47336570 CCAAGATATC
Statistics
Matches: 296, Mismatches: 14, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
46 219 0.74
47 77 0.26
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (46 bp):
AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
Found at i:47338854 original size:16 final size:16
Alignment explanation
Indices: 47338814--47338846 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
47338804 GGTGCTTATT
47338814 CCCAAAACAAGTAATG
1 CCCAAAACAAGTAATG
47338830 CCCAAAACAAGTAATG
1 CCCAAAACAAGTAATG
47338846 C
1 C
47338847 TGATAACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.27, G:0.12, T:0.12
Consensus pattern (16 bp):
CCCAAAACAAGTAATG
Found at i:47341062 original size:12 final size:12
Alignment explanation
Indices: 47341045--47341083 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
47341035 AATAGTTAAC
*
47341045 AATGATAATGAT
1 AATGATAATAAT
47341057 AATGATAATAAT
1 AATGATAATAAT
*
47341069 AATAATAATAAT
1 AATGATAATAAT
47341081 AAT
1 AAT
47341084 AGATGATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (12 bp):
AATGATAATAAT
Found at i:47341069 original size:3 final size:3
Alignment explanation
Indices: 47341049--47341084 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
47341039 GTTAACAATG
* *
47341049 ATA ATG ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
47341085 GATGATGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:47342577 original size:23 final size:24
Alignment explanation
Indices: 47342547--47342594 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
47342537 ATGTCCTATG
47342547 TCTTTCTTT-TTCTTTTCTTTTTT
1 TCTTTCTTTCTTCTTTTCTTTTTT
* *
47342570 TCTTTCTTTCTTTTTTTTTTTTTT
1 TCTTTCTTTCTTCTTTTCTTTTTT
47342594 T
1 T
47342595 GCAAAGTCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (24 bp):
TCTTTCTTTCTTCTTTTCTTTTTT
Found at i:47342587 original size:17 final size:17
Alignment explanation
Indices: 47342555--47342586 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
47342545 TGTCTTTCTT
47342555 TTTCTTTTCTTTTTTTC
1 TTTCTTTTCTTTTTTTC
47342572 TTTC-TTTCTTTTTTT
1 TTTCTTTTCTTTTTTT
47342587 TTTTTTTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTCTTTTCTTTTTTTC
Found at i:47342594 original size:8 final size:8
Alignment explanation
Indices: 47342559--47342593 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
47342549 TTTCTTTTTC
47342559 TTTTCTTT
1 TTTTCTTT
47342567 TTTTCTTT
1 TTTTCTTT
*
47342575 CTTTCTTT
1 TTTTCTTT
47342583 TTTT-TTT
1 TTTTCTTT
47342590 TTTT
1 TTTT
47342594 TGCAAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTCTTT
Found at i:47348895 original size:14 final size:13
Alignment explanation
Indices: 47348863--47348896 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
47348853 ATTAATATGA
47348863 TATTTTTAGAAAT
1 TATTTTTAGAAAT
47348876 TATTTTTAGAAAT
1 TATTTTTAGAAAT
47348889 TATTTTTA
1 TATTTTTA
47348897 AAGTCACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (13 bp):
TATTTTTAGAAAT
Found at i:47349307 original size:19 final size:19
Alignment explanation
Indices: 47349283--47349337 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 19
47349273 ATTTCAAAAA
47349283 TAATATTATTTTAATAGTT
1 TAATATTATTTTAATAGTT
47349302 TAATATTAATTTT-A-AG-T
1 TAATATT-ATTTTAATAGTT
*
47349319 TAATATTTATCTTAATAGT
1 TAATA-TTATTTTAATAGT
47349338 ATTTTATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
17 10 0.33
18 5 0.17
19 10 0.33
20 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (19 bp):
TAATATTATTTTAATAGTT
Found at i:47349358 original size:11 final size:11
Alignment explanation
Indices: 47349283--47349358 Score: 50
Period size: 11 Copynumber: 6.8 Consensus size: 11
47349273 ATTTCAAAAA
*
47349283 TAATATTATTT
1 TAATATTAATT
47349294 TAATAGTTTAATAT
1 TAATA--TTAAT-T
* *
47349308 TAATTTTAAGT
1 TAATATTAATT
*
47349319 TAATATTTATCT
1 TAATATTAAT-T
*
47349331 TAATAGT-ATT
1 TAATATTAATT
47349341 T--TATTAATT
1 TAATATTAATT
47349350 TAATATTAA
1 TAATATTAA
47349359 AGTAATTATC
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 2 0.04
11 21 0.42
12 11 0.22
13 4 0.08
14 5 0.10
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:47352287 original size:46 final size:45
Alignment explanation
Indices: 47352143--47352351 Score: 181
Period size: 46 Copynumber: 4.5 Consensus size: 45
47352133 ATTGTGAACT
** * * *
47352143 AGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATAAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCC-TACGAGACGAGTC
* * * *
47352189 AGTGTAACACCATGTCTGGGACATGGCATCAGCAT-TGAGACGAGTGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTACGAGACGAGT-C
47352236 TAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGTAAGTC
1 -AGTGTAAGACATGTCTGGGACATGCATCGGCCTACGAGACG--AGTC
* * * * * *
47352283 AGTGTAAGACGTGTCTGAGACATGCATTGG-CTACGAGATGTGTT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTACGAGACGAGTC
*
47352327 AGTGCAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
47352352 GCATTGGCAC
Statistics
Matches: 135, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
44 10 0.07
45 15 0.11
46 61 0.45
47 31 0.23
48 18 0.13
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTACGAGACGAGTC
Found at i:47356221 original size:6 final size:6
Alignment explanation
Indices: 47356203--47356290 Score: 56
Period size: 6 Copynumber: 14.3 Consensus size: 6
47356193 AAAAAATATT
* * *
47356203 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACAGA ATTAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * *
47356252 ATCAGA ATCAGT ATGAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
47356291 GTGAATGCAA
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
5 4 0.06
6 51 0.82
7 5 0.08
8 2 0.03
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:47356253 original size:31 final size:31
Alignment explanation
Indices: 47356212--47356290 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
47356202 TATCAGAACT
* *
47356212 AGAATCAGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGAATGAGGTAAC
* *
47356243 AGAATTAGAATCAGAATCAGTATGAGGTAAC
1 AGAATCAGAATCAGAATCAGAATGAGGTAAC
*
47356274 AGAATCAAAATCAGAAT
1 AGAATCAGAATCAGAAT
47356291 GTGAATGCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.20
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGAATGAGGTAAC
Found at i:47356793 original size:27 final size:27
Alignment explanation
Indices: 47356737--47356950 Score: 218
Period size: 27 Copynumber: 8.0 Consensus size: 27
47356727 GGGTAAAATG
* * * *
47356737 GTAATTTTACCCCACAA-GGTATCTCG
1 GTAATTCTACCCTACAAGGGTATTTCA
*
47356763 GTAATTCTACCTTAC-AGGAGTATTTCA
1 GTAATTCTACCCTACAAGG-GTATTTCA
* *
47356790 GTAATTCTACCCTATAGGGGTATTT-A
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
47356816 GGTATTTCTACCCTACAAGGGTATTTCG
1 -GTAATTCTACCCTACAAGGGTATTTCA
* *
47356844 GTAATTCTACCCTACAAGGGTGTTTTA
1 GTAATTCTACCCTACAAGGGTATTTCA
* **
47356871 GTAATTCTACCCTACAGGGGTATTTTG
1 GTAATTCTACCCTACAAGGGTATTTCA
* **
47356898 GTACTTCTACCCTACAAGGGTATTTTG
1 GTAATTCTACCCTACAAGGGTATTTCA
* *
47356925 GCATTTCTACCCTACAAGGGTATTTC
1 GTAATTCTACCCTACAAGGGTATTTC
47356951 GATAATTTTG
Statistics
Matches: 159, Mismatches: 24, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
25 1 0.01
26 14 0.09
27 142 0.89
28 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCA
Found at i:47356854 original size:81 final size:81
Alignment explanation
Indices: 47356740--47356950 Score: 293
Period size: 81 Copynumber: 2.6 Consensus size: 81
47356730 TAAAATGGTA
* * *
47356740 ATTT-TACCCCACAA-GGTATCTCGGTAATTCTACCTTAC-AGGAGTATTTCAGTAATTCTACCC
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGG-GTATTTCAGTAATTCTACCC
*
47356802 TATAGGGGTATTTAGGT
65 TACAGGGGTATTTAGGT
* *
47356819 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTGTTTTAGTAATTCTACCCT
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCT
*
47356884 ACAGGGGTATTTTGGT
66 ACAGGGGTATTTAGGT
* * * *
47356900 ACTTCTACCCTACAAGGGTATTTTGGCATTTCTACCCTACAAGGGTATTTC
1 ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTC
47356951 GATAATTTTG
Statistics
Matches: 116, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
79 4 0.03
80 9 0.08
81 100 0.86
82 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (81 bp):
ATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCT
ACAGGGGTATTTAGGT
Found at i:47356971 original size:27 final size:27
Alignment explanation
Indices: 47356941--47357257 Score: 105
Period size: 27 Copynumber: 11.7 Consensus size: 27
47356931 CTACCCTACA
*
47356941 AGGGTATTTCGATAATTTTGTAAATCG
1 AGGGTATTTCGATAATTTTATAAATCG
** ** * * *
47356968 AGGGTAAAAT-GGCAATTCTGTAAATCA
1 AGGGT-ATTTCGATAATTTTATAAATCG
* * * *
47356995 ATGGTACTTT-GGTAATTTTACAAGTCG
1 AGGGTA-TTTCGATAATTTTATAAATCG
* **
47357022 AGGGTATTTCAATAATTTTATAGGTCG
1 AGGGTATTTCGATAATTTTATAAATCG
* *
47357049 AGGGTATTTC-AGTAATTTCACAAATC-
1 AGGGTATTTCGA-TAATTTTATAAATCG
* * * *
47357075 AGGGATATTTTGGTAATTTTACAAA-CT
1 AGGG-TATTTCGATAATTTTATAAATCG
* * *
47357102 AGGGGTATTTTGATAATTTTACAAA-CT
1 A-GGGTATTTCGATAATTTTATAAATCG
* * * *
47357129 AGGGGTATTTTGGTAATTTTACAAA-CTA
1 A-GGGTATTTCGATAATTTTATAAATC-G
* * *
47357157 AGGGTATTTTGGTAATTTTATAAA-CA
1 AGGGTATTTCGATAATTTTATAAATCG
* * *
47357183 ATGGGTATTT-TAGTAATTTTACAAA-CT
1 A-GGGTATTTCGA-TAATTTTATAAATCG
* * * * *
47357210 AGGAGTATTTTGGTAATTTTGTAAACCA
1 AGG-GTATTTCGATAATTTTATAAATCG
* *
47357238 AGGGTATTTTGGTAATTTTA
1 AGGGTATTTCGATAATTTTA
47357258 CAAACCAGGG
Statistics
Matches: 235, Mismatches: 41, Indels: 28
0.77 0.13 0.09
Matches are distributed among these distances:
26 14 0.06
27 211 0.90
28 10 0.04
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTATAAATCG
Found at i:47357108 original size:81 final size:79
Alignment explanation
Indices: 47356997--47357336 Score: 331
Period size: 81 Copynumber: 4.2 Consensus size: 79
47356987 GTAAATCAAT
* * * * * ** * *
47356997 GGTACTTTGGTAATTTTAC-AAGTCGAGGGTATTTCAATAATTTTATAGGTCGAGGGTATTTCAG
1 GGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTAATAATTTTACA-AACTAGGGTATTTTAG
* *
47357061 TAATTTCACAAATCAG
64 TAATTTTACAAACCAG
* *
47357077 GGATATTTTGGTAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAACTAGGGGTATTTTGG
1 GG-TATTTTGGTAATTTTACAAACTAGGGGTATTTTAATAATTTTACAAACTA-GGGTATTTTAG
*
47357142 TAATTTTACAAACTAAG
64 TAATTTTACAAAC-CAG
* * * * *
47357159 GGTATTTTGGTAATTTTATAAACAATGGGTATTTTAGTAATTTTACAAACTAGGAGTATTTTGGT
1 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAATAATTTTACAAACTAGG-GTATTTTAGT
**
47357224 AATTTTGTAAACCAAG
65 AATTTTACAAACC-AG
* * ** * * * *
47357240 GGTATTTTGGTAATTTTACAAACCAGGGGCATTTTGGTGATTTTATAAACCAATGGTATTTTAGT
1 GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAATAATTTTACAAA-CTAGGGTATTTTAGT
47357305 AATTTTACAAACCAG
65 AATTTTACAAACCAG
47357320 AGGTATTTTGGTAATTT
1 -GGTATTTTGGTAATTT
47357337 GGTAAACTAA
Statistics
Matches: 218, Mismatches: 34, Indels: 15
0.82 0.13 0.06
Matches are distributed among these distances:
80 8 0.04
81 199 0.91
82 11 0.05
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (79 bp):
GGTATTTTGGTAATTTTACAAACTAGGGGTATTTTAATAATTTTACAAACTAGGGTATTTTAGTA
ATTTTACAAACCAG
Found at i:47357262 original size:27 final size:27
Alignment explanation
Indices: 47357049--47357336 Score: 323
Period size: 27 Copynumber: 10.7 Consensus size: 27
47357039 TTATAGGTCG
** * *
47357049 AGGGTATTTCAGTAATTTCACAAATC-
1 AGGGTATTTTGGTAATTTTACAAACCA
*
47357075 AGGGATATTTTGGTAATTTTACAAACTA
1 AGGG-TATTTTGGTAATTTTACAAACCA
* * *
47357103 GGGGTATTTTGATAATTTTACAAACTA
1 AGGGTATTTTGGTAATTTTACAAACCA
* *
47357130 GGGGTATTTTGGTAATTTTACAAACTA
1 AGGGTATTTTGGTAATTTTACAAACCA
*
47357157 AGGGTATTTTGGTAATTTTATAAA-CA
1 AGGGTATTTTGGTAATTTTACAAACCA
* *
47357183 ATGGGTATTTTAGTAATTTTACAAA-CT
1 A-GGGTATTTTGGTAATTTTACAAACCA
**
47357210 AGGAGTATTTTGGTAATTTTGTAAACCA
1 AGG-GTATTTTGGTAATTTTACAAACCA
47357238 AGGGTATTTTGGTAATTTTACAAACCA
1 AGGGTATTTTGGTAATTTTACAAACCA
* * * *
47357265 GGGGCATTTTGGTGATTTTATAAACCA
1 AGGGTATTTTGGTAATTTTACAAACCA
* *
47357292 ATGGTATTTTAGTAATTTTACAAACC-
1 AGGGTATTTTGGTAATTTTACAAACCA
47357318 AGAGGTATTTTGGTAATTT
1 AG-GGTATTTTGGTAATTT
47357337 GGTAAACTAA
Statistics
Matches: 224, Mismatches: 32, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
26 9 0.04
27 208 0.93
28 7 0.03
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.40
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTACAAACCA
Found at i:47357935 original size:17 final size:17
Alignment explanation
Indices: 47357913--47357953 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
47357903 TTGCCACTAA
*
47357913 GCCACAAGGCTTTTTGT
1 GCCACAAGGCCTTTTGT
47357930 GCCACAAGGCCTTTTGT
1 GCCACAAGGCCTTTTGT
*
47357947 GTCACAA
1 GCCACAA
47357954 TTTCTCCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (17 bp):
GCCACAAGGCCTTTTGT
Found at i:47362935 original size:34 final size:34
Alignment explanation
Indices: 47362897--47362963 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
47362887 GAAGTATTTA
47362897 TATACAAAAGCCAATTGTGAGGATGATTATCCAC
1 TATACAAAAGCCAATTGTGAGGATGATTATCCAC
47362931 TATACAAAAGCCAATTGTGAGGATGATTATCCA
1 TATACAAAAGCCAATTGTGAGGATGATTATCCA
47362964 TTTACTTACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (34 bp):
TATACAAAAGCCAATTGTGAGGATGATTATCCAC
Found at i:47364820 original size:29 final size:29
Alignment explanation
Indices: 47364778--47364834 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
47364768 TGCGGGAAAG
47364778 ACAACTTACTTCAGTAGATAAAATAAATA
1 ACAACTTACTTCAGTAGATAAAATAAATA
47364807 ACAACTTACTTCAGTAGATAAAATAAAT
1 ACAACTTACTTCAGTAGATAAAATAAAT
47364835 GAGCCCATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (29 bp):
ACAACTTACTTCAGTAGATAAAATAAATA
Found at i:47368058 original size:23 final size:23
Alignment explanation
Indices: 47368028--47368077 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
47368018 ATTTTATGGG
**
47368028 AGCCTTTGTGGTTGTTCTGTGGA
1 AGCCTTTGTGGTTGTTCTAAGGA
47368051 AGCCTTTGTGGTTGTTCTAAGGA
1 AGCCTTTGTGGTTGTTCTAAGGA
47368074 AGCC
1 AGCC
47368078 CATATGGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.14, C:0.16, G:0.32, T:0.38
Consensus pattern (23 bp):
AGCCTTTGTGGTTGTTCTAAGGA
Found at i:47369685 original size:42 final size:41
Alignment explanation
Indices: 47369588--47369736 Score: 156
Period size: 42 Copynumber: 3.5 Consensus size: 41
47369578 TGCCAACATC
* * * *
47369588 CCAGATGTGGTCTTACATGTAATCAAATGTCGATGCCACTGTT
1 CCAGACGTGGTCTTACACGAAATCAAA-GTCGATGCCAATG-T
**
47369631 CCAGACAAGGTCTTACACGAAATC-AAGTACGATGCCAATGT
1 CCAGACGTGGTCTTACACGAAATCAAAGT-CGATGCCAATGT
* *
47369672 CCTAGACGTGGTCTTACACGTAAATCATAAGTTGATGCCAACGT
1 CC-AGACGTGGTCTTACACG-AAATCA-AAGTCGATGCCAATGT
47369716 CCCAGACGTGGTCTTACACGA
1 -CCAGACGTGGTCTTACACGA
47369737 TAACACATAT
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
41 5 0.06
42 27 0.30
43 25 0.28
44 27 0.30
45 6 0.07
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.26
Consensus pattern (41 bp):
CCAGACGTGGTCTTACACGAAATCAAAGTCGATGCCAATGT
Found at i:47369723 original size:44 final size:43
Alignment explanation
Indices: 47369577--47369735 Score: 173
Period size: 43 Copynumber: 3.7 Consensus size: 43
47369567 AGCTTGTACA
* * *
47369577 ATGCCAACATCCCAGATGTGGTCTTACATGT-AATCAAATGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCAAA-GTCG
* **
47369620 ATGCC-ACTGTTCCAGACAAGGTCTTACACG-AAATC-AAGTACG
1 ATGCCAAC-GTCCCAGACGTGGTCTTACACGTAAATCAAAGT-CG
* * *
47369662 ATGCCAATGTCCTAGACGTGGTCTTACACGTAAATCATAAGTTG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCA-AAGTCG
47369706 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
47369736 ATAACACATA
Statistics
Matches: 95, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
41 2 0.02
42 29 0.31
43 31 0.33
44 29 0.31
45 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCAAAGTCG
Found at i:47373242 original size:21 final size:21
Alignment explanation
Indices: 47373216--47373256 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
47373206 CTACATGCTC
47373216 ATGTGAAGACCACACACGCCG
1 ATGTGAAGACCACACACGCCG
* * *
47373237 ATGTGATGGCCATACACGCC
1 ATGTGAAGACCACACACGCC
47373257 CAAGTGAGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (21 bp):
ATGTGAAGACCACACACGCCG
Found at i:47375277 original size:33 final size:33
Alignment explanation
Indices: 47375231--47375294 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
47375221 ACATGTGAAA
* *
47375231 GAAAGAAACTATAGTGAGGATCAAAAACATTTT
1 GAAACAAAATATAGTGAGGATCAAAAACATTTT
47375264 GAAACAAAATATAGTGAGGATCAAAAACATT
1 GAAACAAAATATAGTGAGGATCAAAAACATT
47375295 GTGAGAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.22
Consensus pattern (33 bp):
GAAACAAAATATAGTGAGGATCAAAAACATTTT
Found at i:47375298 original size:18 final size:18
Alignment explanation
Indices: 47375244--47375299 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
47375234 AGAAACTATA
47375244 GTGAGGATCAAAAACATT
1 GTGAGGATCAAAAACATT
* * * *
47375262 TTGA--AAC-AAAATATA
1 GTGAGGATCAAAAACATT
47375277 GTGAGGATCAAAAACATT
1 GTGAGGATCAAAAACATT
47375295 GTGAG
1 GTGAG
47375300 AGAAAAAAAT
Statistics
Matches: 27, Mismatches: 8, Indels: 6
0.66 0.20 0.15
Matches are distributed among these distances:
15 9 0.33
16 2 0.07
17 2 0.07
18 14 0.52
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.23
Consensus pattern (18 bp):
GTGAGGATCAAAAACATT
Found at i:47385213 original size:17 final size:18
Alignment explanation
Indices: 47385181--47385217 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
47385171 AAGTACTTAT
*
47385181 TATTAAGTTTATATAAAA
1 TATTAAGTTCATATAAAA
47385199 TATTAA-TTCATATAAAA
1 TATTAAGTTCATATAAAA
47385216 TA
1 TA
47385218 AATTTTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
TATTAAGTTCATATAAAA
Found at i:47393350 original size:129 final size:129
Alignment explanation
Indices: 47393162--47393432 Score: 366
Period size: 136 Copynumber: 2.1 Consensus size: 129
47393152 TTCTTATTGA
* * *
47393162 TTGATTTAGTTGTTCTTAGTTCTTTAAACTACGGTCTTCACTTTTGTGTTCTTTCAGTTC-AATT
1 TTGATTTTGTTGTTCTTAGCTCTTTAAACTACAGTCTTCACTTTTGTGTTCTTTCAGTTCAAATT
*
47393226 AAAATGGGTTTGTTTGTTTTTA-CTTTTTCTGTACTATTTGATTCTTATTGATTGCCCCTTTTG
66 AAAATGGGTTTGTCTGTTTTTATCTTTTTCTGTACTATTTGATTCTTATTGATTGCCCCTTTTG
* **
47393289 TTGATTTTGTTGTTCTTAGCTCTTTGTAAATTACAGTCTTTGCTTTTGTGTTCTTTCAGTTCAAA
1 TTGATTTTGTTGTTCTTAGCTC-TT-TAAACTACAGTCTTCACTTTTGTGTTCTTTCAGTTCAAA
* * * *
47393354 TTTAAATGGGTTTGTCTGTTTTTACTTCTTCTTTTTTTGTACTGTTTGATTCTTATTGATTGCTC
64 TTAAAATGGGTTTGTCTGTTTTTA-----TCTTTTTCTGTACTATTTGATTCTTATTGATTGCCC
47393419 CTTTTG
124 CTTTTG
47393425 TTGATTTT
1 TTGATTTT
47393433 ACTATTTTTA
Statistics
Matches: 124, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
127 20 0.16
128 2 0.02
129 32 0.26
130 24 0.19
136 46 0.37
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.56
Consensus pattern (129 bp):
TTGATTTTGTTGTTCTTAGCTCTTTAAACTACAGTCTTCACTTTTGTGTTCTTTCAGTTCAAATT
AAAATGGGTTTGTCTGTTTTTATCTTTTTCTGTACTATTTGATTCTTATTGATTGCCCCTTTTG
Found at i:47393444 original size:136 final size:129
Alignment explanation
Indices: 47393202--47393496 Score: 349
Period size: 136 Copynumber: 2.2 Consensus size: 129
47393192 ACGGTCTTCA
*
47393202 CTTTTGTGTTCTTTCAGTTCAATTAAAATGGGTTTGTTTGTTTTTACTTTTTCTGTACTATTTGA
1 CTTTTGTGTTCTTTCAGTTCAATTAAAATGGGTTTGTCTGTTTTTACTTTTTCTGTACTATTTGA
** *
47393267 TTCTTATTGATTGCCCCTTTTGTTGATTTTGTTGTTCTTAGCTCTTTGTAAATTACAGTCTTTG
66 TTCTTATTGATTGCCCCTTTTGTTGATTTTACTATTCTTAGCTCTTTGTAAATTACAGTCTTTG
* *
47393331 CTTTTGTGTTCTTTCAGTTCAAATTTAAATGGGTTTGTCTGTTTTTACTTCTTCTTTTTTTGTAC
1 CTTTTGTGTTCTTTCAGTTC-AATTAAAATGGGTTTGTCTGTTTTTA------CTTTTTCTGTAC
* * * * * * *
47393396 TGTTTGATTCTTATTGATTGCTCCTTTTGTTGATTTTACTATTTTTAGCTATTGGCAAACTGCAC
59 TATTTGATTCTTATTGATTGCCCCTTTTGTTGATTTTACTATTCTTAGCTCTTTGTAAA-T-TAC
*
47393461 A-ACATTTG
122 AGTC-TTTG
*
47393469 CTTTTTGTGTTCTTTCAGCTCAATTAAA
1 C-TTTTGTGTTCTTTCAGTTCAATTAAA
47393497 GACTAAATTT
Statistics
Matches: 139, Mismatches: 16, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
129 20 0.14
130 24 0.17
136 61 0.44
137 2 0.01
138 14 0.10
139 18 0.13
ACGTcount: A:0.17, C:0.14, G:0.15, T:0.54
Consensus pattern (129 bp):
CTTTTGTGTTCTTTCAGTTCAATTAAAATGGGTTTGTCTGTTTTTACTTTTTCTGTACTATTTGA
TTCTTATTGATTGCCCCTTTTGTTGATTTTACTATTCTTAGCTCTTTGTAAATTACAGTCTTTG
Found at i:47393789 original size:30 final size:30
Alignment explanation
Indices: 47393753--47393849 Score: 158
Period size: 30 Copynumber: 3.2 Consensus size: 30
47393743 GGTTTGAAGT
47393753 TTTATATGAGCATGCTGGGAAGGGTATAGG
1 TTTATATGAGCATGCTGGGAAGGGTATAGG
*
47393783 TTTATATGAGCATGCTGGGAAGGGTATAAG
1 TTTATATGAGCATGCTGGGAAGGGTATAGG
*
47393813 TTTATATAAGCATATGCTGGGAAGGGTATAGG
1 TTTATATGAGC--ATGCTGGGAAGGGTATAGG
47393845 TTTAT
1 TTTAT
47393850 GTATTTAAAC
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
30 39 0.63
32 23 0.37
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.33
Consensus pattern (30 bp):
TTTATATGAGCATGCTGGGAAGGGTATAGG
Found at i:47396114 original size:32 final size:29
Alignment explanation
Indices: 47396078--47396148 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 29
47396068 CACCTATTAT
* *
47396078 TTAAAATAGTTGTTGTTTAGAATAACTATTGG
1 TTAAAATAGTT-ATGTTCAGAATAACT-TT-G
47396110 TTAAAGATAGTTATGTTCAGAATAACTTTG
1 TTAAA-ATAGTTATGTTCAGAATAACTTTG
47396140 TTCAAAATA
1 TT-AAAATA
47396149 AGGCTATAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 6 0.17
31 5 0.14
32 18 0.51
33 6 0.17
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (29 bp):
TTAAAATAGTTATGTTCAGAATAACTTTG
Found at i:47401039 original size:6 final size:7
Alignment explanation
Indices: 47401014--47401038 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
47401004 ACCTTCAAGC
47401014 AAAAAGA
1 AAAAAGA
47401021 AAAAAGA
1 AAAAAGA
47401028 AAAAAGA
1 AAAAAGA
47401035 AAAA
1 AAAA
47401039 GTTTGACCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:47407621 original size:16 final size:16
Alignment explanation
Indices: 47407600--47407630 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47407590 TTTACTATTA
*
47407600 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
47407616 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
47407631 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:47419326 original size:61 final size:62
Alignment explanation
Indices: 47419223--47419346 Score: 223
Period size: 61 Copynumber: 2.0 Consensus size: 62
47419213 ATCCCAAAAA
47419223 TCAGAGTTACCCATCATTTCCACCAACCAACCACTTAGAATTTAGCTACTCATGGTTATATT
1 TCAGAGTTACCCATCATTTCCACCAACCAACCACTTAGAATTTAGCTACTCATGGTTATATT
* *
47419285 TCAGAGTTACCCATCATTTCCACCAA-CGACCACTTAGAATTTAGCTACTCATTGTTATATT
1 TCAGAGTTACCCATCATTTCCACCAACCAACCACTTAGAATTTAGCTACTCATGGTTATATT
47419346 T
1 T
47419347 AAACTCATTG
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 34 0.57
62 26 0.43
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.34
Consensus pattern (62 bp):
TCAGAGTTACCCATCATTTCCACCAACCAACCACTTAGAATTTAGCTACTCATGGTTATATT
Found at i:47431281 original size:47 final size:50
Alignment explanation
Indices: 47431227--47431320 Score: 131
Period size: 47 Copynumber: 1.9 Consensus size: 50
47431217 ATTCCAAAAA
* *
47431227 TAATATTATTTTAATATTTTAATATTAAA-TTA-AAT-TTAATATTATCT
1 TAATATTATTTCAATAGTTTAATATTAAAGTTATAATCTTAATATTATCT
* *
47431274 TAATATTATTTCATTAGTTTAATATTAAAGTTATTATCTTAATATTA
1 TAATATTATTTCAATAGTTTAATATTAAAGTTATAATCTTAATATTA
47431321 AATTTAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
47 26 0.65
48 3 0.08
49 2 0.05
50 9 0.22
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.54
Consensus pattern (50 bp):
TAATATTATTTCAATAGTTTAATATTAAAGTTATAATCTTAATATTATCT
Found at i:47431315 original size:20 final size:20
Alignment explanation
Indices: 47431266--47431322 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
47431256 TTAAATTTAA
*
47431266 TATTATCTTAATATT--ATT
1 TATTATCTTAATATTAAAGT
47431284 TCATTAGT-TTAATATTAAAGT
1 T-ATTA-TCTTAATATTAAAGT
47431305 TATTATCTTAATATTAAA
1 TATTATCTTAATATTAAA
47431323 TTTAATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 1 0.03
19 13 0.39
20 16 0.48
21 3 0.09
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.53
Consensus pattern (20 bp):
TATTATCTTAATATTAAAGT
Found at i:47432489 original size:16 final size:16
Alignment explanation
Indices: 47432468--47432500 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
47432458 CAAGATAATG
47432468 TGGTATTATCTTAGAA
1 TGGTATTATCTTAGAA
47432484 TGGTATTATCTTAGAA
1 TGGTATTATCTTAGAA
47432500 T
1 T
47432501 AGGTGTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (16 bp):
TGGTATTATCTTAGAA
Found at i:47456220 original size:11 final size:11
Alignment explanation
Indices: 47456204--47456231 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
47456194 AGAATACTTC
47456204 AATAAAAAATA
1 AATAAAAAATA
47456215 AATAAAAAATA
1 AATAAAAAATA
47456226 AATAAA
1 AATAAA
47456232 CTCTTGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AATAAAAAATA
Found at i:47458650 original size:18 final size:18
Alignment explanation
Indices: 47458627--47458663 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
47458617 AACGATCCTC
*
47458627 TATCAAATAATTAATTAT
1 TATCAAACAATTAATTAT
47458645 TATCAAACAATTAATTAT
1 TATCAAACAATTAATTAT
47458663 T
1 T
47458664 CCCTCCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (18 bp):
TATCAAACAATTAATTAT
Found at i:47461167 original size:49 final size:48
Alignment explanation
Indices: 47461016--47461191 Score: 178
Period size: 49 Copynumber: 3.6 Consensus size: 48
47461006 GGATAAGATG
* *
47461016 TCGACGCCATGTCCCAGACATAGTCTTACACTGGCTAG-CA-C-ATCAAA
1 TCGATGCCATGTCCCAGACA-AGTCTTACACTGGCT-GTCATCTATCGAA
* * * * * * *
47461063 TCGATGCCATGTCCTAGACAGGTCTTACACTGACTTTCATATATTGAGG
1 TCGATGCCATGTCCCAGACAAGTCTTACACTGGCTGTCATCTATCGA-A
* * *
47461112 TTGATGCCGTGTCCCAGACAGGTCTTACACTGGCTGTCATCTATCGGAA
1 TCGATGCCATGTCCCAGACAAGTCTTACACTGGCTGTCATCTATC-GAA
*
47461161 TCGATGCCATGTCCCAGATAAGTCTTACACT
1 TCGATGCCATGTCCCAGACAAGTCTTACACT
47461192 AACACACAAC
Statistics
Matches: 103, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
46 15 0.15
47 18 0.17
48 3 0.03
49 65 0.63
50 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (48 bp):
TCGATGCCATGTCCCAGACAAGTCTTACACTGGCTGTCATCTATCGAA
Found at i:47461279 original size:48 final size:47
Alignment explanation
Indices: 47461218--47461381 Score: 163
Period size: 48 Copynumber: 3.5 Consensus size: 47
47461208 ACGCCATGTA
* **
47461218 CTAGACAAGTCTTACACTAGCTTGTATATCTCGAGGTTGATGCGTCTC
1 CTAGACATGTCTTACACTAGCTTGTATATCTCGAGGCCGATGCGT-TC
* ** * * *
47461266 CTAGACATGTCTTACACTAGC-TCT-CGTCTCAAAGCCGATGCATGTC
1 CTAGACATGTCTTACACTAGCTTGTATATCTCGAGGCCGATGCGT-TC
* *
47461312 CTAGACATGTCTTACACTGGCTGGTATATCTCGAGGCCGATGCATGTTC
1 CTAGACATGTCTTACACTAGCTTGTATATCTCGAGGCCGATGC--GTTC
*
47461361 C-AGACATGTCTTACACCAGCT
1 CTAGACATGTCTTACACTAGCT
47461382 CTCGTAATGT
Statistics
Matches: 92, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
46 34 0.37
47 3 0.03
48 51 0.55
49 3 0.03
50 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (47 bp):
CTAGACATGTCTTACACTAGCTTGTATATCTCGAGGCCGATGCGTTC
Found at i:47461324 original size:94 final size:93
Alignment explanation
Indices: 47461212--47461386 Score: 253
Period size: 94 Copynumber: 1.9 Consensus size: 93
47461202 AAGCTGACGC
* **
47461212 CATGTACTAGACAAGTCTTACACTAGCTTGTATATCTCGAGGTTGATGC-GTCTCCTAGACATGT
1 CATGTACTAGACAAGTCTTACACTAGCTGGTATATCTCGAGGCCGATGCAGT-TCC-AGACATGT
*
47461276 CTTACACTAGCTCTCGTCTCAAAGCCGATG
64 CTTACACCAGCTCTCGTCTCAAAGCCGATG
* * *
47461306 CATGTCCTAGACATGTCTTACACTGGCTGGTATATCTCGAGGCCGATGCATGTTCCAGACATGTC
1 CATGTACTAGACAAGTCTTACACTAGCTGGTATATCTCGAGGCCGATGCA-GTTCCAGACATGTC
47461371 TTACACCAGCTCTCGT
65 TTACACCAGCTCTCGT
47461387 AATGTGGCTG
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
94 67 0.93
95 3 0.04
96 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (93 bp):
CATGTACTAGACAAGTCTTACACTAGCTGGTATATCTCGAGGCCGATGCAGTTCCAGACATGTCT
TACACCAGCTCTCGTCTCAAAGCCGATG
Found at i:47461412 original size:94 final size:94
Alignment explanation
Indices: 47461220--47461426 Score: 240
Period size: 94 Copynumber: 2.2 Consensus size: 94
47461210 GCCATGTACT
* * ** *
47461220 AGACAAGTCTTACACTAGCTTGTATATCTCGAGGTTGATGCGTCTCCTAGACATGTCTTACACTA
1 AGACAAGTCTTACACTGGCTGGTATATCTCGAGGCCGATGCGTCTCCTAGACATGTCTTACACCA
* * *
47461285 GCTCTCGTCTCAAAGCCGATGCATGTCCT
66 GCTCTCGTATCAAAGCCGATGCATCTCCC
*
47461314 AGACATGTCTTACACTGGCTGGTATATCTCGAGGCCGATGCATGT-TCC-AGACATGTCTTACAC
1 AGACAAGTCTTACACTGGCTGGTATATCTCGAGGCCGATGC--GTCTCCTAGACATGTCTTACAC
*** *
47461377 CAGCTCTCGTAAT-GTGGCTGATGCATCTCCC
64 CAGCTCTCGT-ATCAAAGCCGATGCATCTCCC
*
47461408 AGACACGTCTTACACTGGC
1 AGACAAGTCTTACACTGGC
47461427 ACACGTATCA
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
94 90 0.94
95 4 0.04
96 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.29
Consensus pattern (94 bp):
AGACAAGTCTTACACTGGCTGGTATATCTCGAGGCCGATGCGTCTCCTAGACATGTCTTACACCA
GCTCTCGTATCAAAGCCGATGCATCTCCC
Found at i:47464252 original size:18 final size:18
Alignment explanation
Indices: 47464229--47464264 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
47464219 TTCCTGGATG
47464229 GTAGTCGATTATCAACTC
1 GTAGTCGATTATCAACTC
**
47464247 GTAGTCTTTTATCAACTC
1 GTAGTCGATTATCAACTC
47464265 TAACCATCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (18 bp):
GTAGTCGATTATCAACTC
Found at i:47466596 original size:46 final size:46
Alignment explanation
Indices: 47466463--47466639 Score: 149
Period size: 46 Copynumber: 3.8 Consensus size: 46
47466453 TGATATGTGT
* * ** *
47466463 GCTAGTGTAAGACATGTTTGGGACATGCATCAGCCAC-ATTATGAGA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCTTCGA-GATGAGA
* * * ** * *
47466509 GCCAGTGTAAGACATGTTTGGGACATTTATCGGCTTTGAGATGAGA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCTTCGAGATGAGA
* * *
47466555 GCTAGTGTAAGACATGTCTAGGACATGCATCAACTTCGAGATATACAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCTTCGAGAT-GA-GA
* * *
47466603 ACTAGTGTAAGACCTGTCTAGGACATGGCGTCAGCTT
1 GCTAGTGTAAGACATGTCTAGGACAT-GCATCAGCTT
47466640 GTTGTGTGTT
Statistics
Matches: 105, Mismatches: 22, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
46 70 0.67
47 2 0.02
48 25 0.24
49 8 0.08
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTAGGACATGCATCAGCTTCGAGATGAGA
Found at i:47466776 original size:49 final size:50
Alignment explanation
Indices: 47466650--47466776 Score: 159
Period size: 49 Copynumber: 2.6 Consensus size: 50
47466640 GTTGTGTGTT
* * *
47466650 GTGTAAAACCTGTCTGGGACATGGCAT-TGACACCGATAAATGAGAGCCA
1 GTGTAAGACCTGTCTGGGACATGGCATCGGACACCGATAAATGAAAGCCA
* * * *
47466699 GTGTAAGACCTGTCTGGGACACGGCATCGGA-ATCGATATATGAAAGTCA
1 GTGTAAGACCTGTCTGGGACATGGCATCGGACACCGATAAATGAAAGCCA
* *
47466748 GTGTAAGACCTCTCTGGGACATGACATCG
1 GTGTAAGACCTGTCTGGGACATGGCATCG
47466777 ACTTTGATGT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
49 65 0.97
50 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (50 bp):
GTGTAAGACCTGTCTGGGACATGGCATCGGACACCGATAAATGAAAGCCA
Found at i:47476882 original size:49 final size:48
Alignment explanation
Indices: 47476774--47476955 Score: 179
Period size: 49 Copynumber: 3.8 Consensus size: 48
47476764 AGGATAAGAT
* * ** * *
47476774 GCCGACGCCATGTCCCAAACATGGTCTTACACTGAC-TAGCACATCAAA
1 GCCGATGCCATGTCCCAGACA-GGTCTTACACTGACTTAATATATCAAG
* *
47476822 GTCGATGCCATGTCCCAGATAGGTCTTACACTGACTTTAATATATCAAG
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGAC-TTAATATATCAAG
* * * * *
47476871 GCCGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATCTATC-GG
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGACT-TAATATATCAAG
* *
47476919 TGTCGATGCCATGTCCCAGACAGGTCTTACATTGACT
1 -GCCGATGCCATGTCCCAGACAGGTCTTACACTGACT
47476956 CACAACAAGC
Statistics
Matches: 111, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
47 14 0.13
48 19 0.17
49 78 0.70
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACAGGTCTTACACTGACTTAATATATCAAG
Found at i:47476944 original size:98 final size:97
Alignment explanation
Indices: 47476774--47476955 Score: 249
Period size: 98 Copynumber: 1.9 Consensus size: 97
47476764 AGGATAAGAT
47476774 GCCGACGCCATGTCCCAAACATGGTCTTACACTGACTAGCACATCAAAGTCGATGCCATGTCCCA
1 GCCGACGCCATGTCCCAAACATGGTCTTACACTGACTAGCACATCAAAGTCGATGCCATGTCCCA
*
47476839 GATAGGTCTTACACTGACTTTAATATATCAAG
66 GACAGGTCTTACACTGACTTTAATATATCAAG
* * * ** ***
47476871 GCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCTCATCTATCGGTGTCGATGCCATGTCC
1 GCCGACGCCATGTCCCAAACATGGTCTTACACTGACTAGCA-C-ATCAAAGTCGATGCCATGTCC
*
47476935 CAGACAGGTCTTACATTGACT
64 CAGACAGGTCTTACACTGACT
47476956 CACAACAAGC
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
96 15 0.21
97 21 0.29
98 37 0.51
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (97 bp):
GCCGACGCCATGTCCCAAACATGGTCTTACACTGACTAGCACATCAAAGTCGATGCCATGTCCCA
GACAGGTCTTACACTGACTTTAATATATCAAG
Found at i:47477045 original size:48 final size:48
Alignment explanation
Indices: 47476980--47477277 Score: 213
Period size: 46 Copynumber: 6.3 Consensus size: 48
47476970 GCCATGTCTT
* * *
47476980 AGACAGGTCTTAAACTAGCTTGTATATCTCGAGACTGATGCATGTTCC
1 AGACATGTCTTACACTAGCTTGTATATCTCGAGACTGATGCATGTCCC
* * ** *
47477028 AGACATGTCATACACTAGC-TCT-CGTCTC-AAAGCTGATGCATGTCCC
1 AGACATGTCTTACACTAGCTTGTATATCTCGAGA-CTGATGCATGTCCC
* * * * **
47477074 AGACATGTCTTACACTGGCTGGTATATCTCGAGGCCGATGCAACTCCC
1 AGACATGTCTTACACTAGCTTGTATATCTCGAGACTGATGCATGTCCC
* * * *
47477122 AAACATGTCTTACACTAGCTCTCGTA-ATGT-G-GTCT-ATGCATGTCAC
1 AGACATGTCTTACACTAGCT-T-GTATATCTCGAGACTGATGCATGTCCC
* * * * **
47477168 AGACATGTCTTACACTGGCTGGTATATCTCGAGGCCGATGCAACTCCC
1 AGACATGTCTTACACTAGCTTGTATATCTCGAGACTGATGCATGTCCC
* * * *
47477216 AAACATGTCTTACACTAGCTCTCGTA-ATGT-G-GCCT-ATGCATGTCAC
1 AGACATGTCTTACACTAGCT-T-GTATATCTCGAGACTGATGCATGTCCC
*
47477262 AGACATGTTTTACACT
1 AGACATGTCTTACACT
47477278 GGCACACGTA
Statistics
Matches: 190, Mismatches: 48, Indels: 26
0.72 0.18 0.10
Matches are distributed among these distances:
44 3 0.02
45 5 0.03
46 83 0.44
47 9 0.05
48 77 0.41
49 7 0.04
50 6 0.03
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (48 bp):
AGACATGTCTTACACTAGCTTGTATATCTCGAGACTGATGCATGTCCC
Found at i:47477084 original size:94 final size:94
Alignment explanation
Indices: 47476980--47477280 Score: 381
Period size: 94 Copynumber: 3.2 Consensus size: 94
47476970 GCCATGTCTT
* * * * * * ** * * *
47476980 AGACAGGTCTTAAACTAGCTTGTATATCTCGAGACTGATGCATGTTCCAGACATGTCATACACTA
1 AGACATGTCTTACACTGGCTGGTATATCTCGAGGCCGATGCAACTCCCAAACATGTCTTACACTA
* *
47477045 GCTCTCGT-CTCAAAG-CTGATGCATGTCCC
66 GCTCTCGTAAT-AAAGTCT-ATGCATGTCAC
47477074 AGACATGTCTTACACTGGCTGGTATATCTCGAGGCCGATGCAACTCCCAAACATGTCTTACACTA
1 AGACATGTCTTACACTGGCTGGTATATCTCGAGGCCGATGCAACTCCCAAACATGTCTTACACTA
***
47477139 GCTCTCGTAATGTGGTCTATGCATGTCAC
66 GCTCTCGTAATAAAGTCTATGCATGTCAC
47477168 AGACATGTCTTACACTGGCTGGTATATCTCGAGGCCGATGCAACTCCCAAACATGTCTTACACTA
1 AGACATGTCTTACACTGGCTGGTATATCTCGAGGCCGATGCAACTCCCAAACATGTCTTACACTA
*** *
47477233 GCTCTCGTAATGTGGCCTATGCATGTCAC
66 GCTCTCGTAATAAAGTCTATGCATGTCAC
*
47477262 AGACATGTTTTACACTGGC
1 AGACATGTCTTACACTGGC
47477281 ACACGTATCA
Statistics
Matches: 187, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
94 184 0.98
95 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (94 bp):
AGACATGTCTTACACTGGCTGGTATATCTCGAGGCCGATGCAACTCCCAAACATGTCTTACACTA
GCTCTCGTAATAAAGTCTATGCATGTCAC
Found at i:47482784 original size:15 final size:15
Alignment explanation
Indices: 47482748--47482827 Score: 74
Period size: 15 Copynumber: 5.4 Consensus size: 15
47482738 GTATCTTGGG
* *
47482748 TTTCTTTATCCTAGA
1 TTTCTTTATTCTGGA
*
47482763 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
47482778 TTCCTTTATTCTGGG
1 TTTCTTTATTCTGGA
*
47482793 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
47482808 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
47482822 TTTCTT
1 TTTCTT
47482828 GTTATCTTTG
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
14 10 0.19
15 40 0.77
16 2 0.04
ACGTcount: A:0.11, C:0.19, G:0.12, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:47485250 original size:46 final size:46
Alignment explanation
Indices: 47485197--47485371 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
47485187 TATTTGGGCA
47485197 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
47485243 TCCGAACTCGTTGAGTTGAGT-CGAGTTCA---A-GAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G
* * *
47485287 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
47485335 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
47485372 GTGGGTTACA
Statistics
Matches: 110, Mismatches: 7, Indels: 24
0.78 0.05 0.17
Matches are distributed among these distances:
41 3 0.03
42 6 0.05
44 1 0.01
45 8 0.07
46 76 0.69
47 8 0.07
48 1 0.01
50 4 0.04
51 3 0.03
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:47485350 original size:92 final size:93
Alignment explanation
Indices: 47485193--47485364 Score: 283
Period size: 92 Copynumber: 1.9 Consensus size: 93
47485183 AGCATATTTG
* * * *
47485193 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCATTGAG
47485258 TTGAGT-CGAGTTCAAGAGATGTAACTA
66 TTGAGTCCGAGTTCAAGAGATGTAACTA
* *
47485285 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAGCTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCATTGAG
47485350 TTGAGTCCGAGTTCA
66 TTGAGTCCGAGTTCA
47485365 CTTATGGGTG
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 65 0.89
93 8 0.11
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCATTGAG
TTGAGTCCGAGTTCAAGAGATGTAACTA
Found at i:47488240 original size:22 final size:22
Alignment explanation
Indices: 47488212--47488333 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
47488202 TTCCACATCC
47488212 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
47488234 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
47488258 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * * *
47488281 ATCTCATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
47488305 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
47488328 ATCACA
1 ATCACA
47488334 CATACACATG
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 26 0.37
23 12 0.17
24 12 0.17
25 20 0.29
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:47488557 original size:49 final size:47
Alignment explanation
Indices: 47488184--47488830 Score: 935
Period size: 47 Copynumber: 13.6 Consensus size: 47
47488174 CCCTTCGGGA
* * *
47488184 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
47488231 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
47488278 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
47488325 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
47488372 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
47488419 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
47488466 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
47488513 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
47488562 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
47488609 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
47488658 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
47488707 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
47488756 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
47488805 CTTATCACATATATACACTTTCACAT
1 CTTATCACATATATACACTTTCACAT
47488831 ATATTCAAAT
Statistics
Matches: 570, Mismatches: 24, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 334 0.59
49 234 0.41
50 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:47490355 original size:56 final size:57
Alignment explanation
Indices: 47490288--47490404 Score: 218
Period size: 57 Copynumber: 2.1 Consensus size: 57
47490278 TATTAGTTTA
47490288 TTGCCCATGCTTCTTATTTTA-TTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTCTTCCATTAACACAACATGTTTCATGACATGTT
*
47490344 TTGCCCATGCTTCTTATTTTATTTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTCTTCCATTAACACAACATGTTTCATGACATGTT
47490401 TTGC
1 TTGC
47490405 TCATCATCCC
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 21 0.36
57 38 0.64
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.46
Consensus pattern (57 bp):
TTGCCCATGCTTCTTATTTTATTTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:47539158 original size:17 final size:17
Alignment explanation
Indices: 47539136--47539171 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
47539126 TTGGGATGTA
*
47539136 AACTCATCAGCATTATC
1 AACTCATAAGCATTATC
47539153 AACTCATAAGCATTATC
1 AACTCATAAGCATTATC
47539170 AA
1 AA
47539172 GACGAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.28
Consensus pattern (17 bp):
AACTCATAAGCATTATC
Found at i:47546569 original size:27 final size:27
Alignment explanation
Indices: 47546539--47546614 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 27
47546529 AAATAACTAA
*
47546539 AATACCCCCATAGGGTAAAATGACCGT
1 AATACCCCTATAGGGTAAAATGACCGT
** * * *
47546566 AATATGCCTATAAGGTATAATGACTGT
1 AATACCCCTATAGGGTAAAATGACCGT
* * *
47546593 AATTCCCTTGTAGGGTAAAATG
1 AATACCCCTATAGGGTAAAATG
47546615 GTTGTTAGTA
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (27 bp):
AATACCCCTATAGGGTAAAATGACCGT
Found at i:47550039 original size:27 final size:26
Alignment explanation
Indices: 47550009--47550100 Score: 85
Period size: 27 Copynumber: 3.5 Consensus size: 26
47549999 ACCCTTAATC
*
47550009 GGGTAAAATGATCGAAATACCCCCATA
1 GGGTAAAATGACCGAAATA-CCCCATA
*
47550036 GGGTAAAATGACCGAAATATCCCATA
1 GGGTAAAATGACCGAAATACCCCATA
* * * * * **
47550062 AGGTATAATGACTGTAATTCTCCTGTA
1 GGGTAAAATGACCGAAATAC-CCCATA
47550089 GGGTAAAATGAC
1 GGGTAAAATGAC
47550101 TGTCTTTCCC
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
26 20 0.38
27 32 0.62
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (26 bp):
GGGTAAAATGACCGAAATACCCCATA
Found at i:47561950 original size:27 final size:27
Alignment explanation
Indices: 47561920--47562009 Score: 121
Period size: 27 Copynumber: 3.3 Consensus size: 27
47561910 GGCTGCAAGA
* *
47561920 ACAGATAATGTGACAGAGTCACCAGAT
1 ACAGATAATGTGGCAGAGCCACCAGAT
*
47561947 ACAGATAATCGTGGCAGAGCCATCAGA-
1 ACAGATAAT-GTGGCAGAGCCACCAGAT
47561974 ACAGATATATGTGGCAGAGCCACCAGAT
1 ACAGATA-ATGTGGCAGAGCCACCAGAT
47562002 A-AGATAAT
1 ACAGATAAT
47562010 TCTGCACCTA
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
26 2 0.04
27 37 0.66
28 17 0.30
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (27 bp):
ACAGATAATGTGGCAGAGCCACCAGAT
Found at i:47562037 original size:27 final size:27
Alignment explanation
Indices: 47562006--47562064 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
47561996 CCAGATAAGA
47562006 TAATTCTGCACCTAGGGGGTATAACAG
1 TAATTCTGCACCTAGGGGGTATAACAG
* *
47562033 TAATTTTTCACCTAGGGGGTATAACAG
1 TAATTCTGCACCTAGGGGGTATAACAG
47562060 TAATT
1 TAATT
47562065 TTCCATACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (27 bp):
TAATTCTGCACCTAGGGGGTATAACAG
Found at i:47562065 original size:27 final size:27
Alignment explanation
Indices: 47562014--47562066 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
47562004 GATAATTCTG
47562014 CACCTAGGGGGTATAACAGTAATTTTT
1 CACCTAGGGGGTATAACAGTAATTTTT
47562041 CACCTAGGGGGTATAACAGTAATTTT
1 CACCTAGGGGGTATAACAGTAATTTT
47562067 CCATACATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (27 bp):
CACCTAGGGGGTATAACAGTAATTTTT
Found at i:47563525 original size:26 final size:26
Alignment explanation
Indices: 47563494--47563549 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
47563484 TGAAATGTCC
47563494 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
47563520 ATCATGGAATATTTACCTCAGCCATT
1 ATCATGGAACATTTACCTAACCCATT
47563546 ATCA
1 ATCA
47563550 ATTTTTATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:47566361 original size:49 final size:49
Alignment explanation
Indices: 47566308--47566402 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
47566298 AATTACTCGA
*
47566308 CAATGATGACTTTTAGTATTTGTTTATTCTGCCATCCCGGGTTGCCCGG
1 CAATGATGACTTTTAGTATTTGTTTATTCTACCATCCCGGGTTGCCCGG
* * **
47566357 CAATGATTATTTTTAGTATTTGTTTATTCTACCATCTTGGGTTGCC
1 CAATGATGACTTTTAGTATTTGTTTATTCTACCATCCCGGGTTGCC
47566403 TAAGAATGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (49 bp):
CAATGATGACTTTTAGTATTTGTTTATTCTACCATCCCGGGTTGCCCGG
Found at i:47566411 original size:49 final size:49
Alignment explanation
Indices: 47566308--47566426 Score: 141
Period size: 49 Copynumber: 2.4 Consensus size: 49
47566298 AATTACTCGA
* **
47566308 CAATGATGACTTTTAGTATTTGTTTATTCTGCCATCCCGGGTTGCCCGG
1 CAATGATGACTTTTAGTATTTGTTTATTCTACCATCCCGGGTTGCCAAG
* * **
47566357 CAATGATTATTTTTAGTATTTGTTTATTCTACCATCTTGGGTTGCCTAAG
1 CAATGATGACTTTTAGTATTTGTTTATTCTACCATCCCGGGTTGCC-AAG
* *
47566407 -AATGACGCCTTTTAGTATTT
1 CAATGATGACTTTTAGTATTT
47566427 TATTATCCTG
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 57 0.98
50 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (49 bp):
CAATGATGACTTTTAGTATTTGTTTATTCTACCATCCCGGGTTGCCAAG
Found at i:47570893 original size:49 final size:52
Alignment explanation
Indices: 47570837--47570934 Score: 157
Period size: 50 Copynumber: 1.9 Consensus size: 52
47570827 TAAACCGCAA
*
47570837 AATAATTAACT-ATTAAATTTAAAT-ATTTAATAAT-TTTCCTTAACATCAT
1 AATAATTAACTAATTAAAATTAAATAATTTAATAATATTTCCTTAACATCAT
*
47570886 AATAATTAACTAATTAAAATTAAATAATTTAATAATATTTTCTTAACAT
1 AATAATTAACTAATTAAAATTAAATAATTTAATAATATTTCCTTAACAT
47570935 TTCTAATTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
49 11 0.25
50 12 0.27
51 10 0.23
52 11 0.25
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (52 bp):
AATAATTAACTAATTAAAATTAAATAATTTAATAATATTTCCTTAACATCAT
Found at i:47571070 original size:28 final size:28
Alignment explanation
Indices: 47571021--47571096 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
47571011 AATCAAAGAG
* * **
47571021 TTTAGAA-AAAAAATTAAAAATTGGGAA
1 TTTAGAATAAAAAATCAAGAATTGACAA
*
47571048 TTTAGAATAAAAAATCGAGAATTGACAA
1 TTTAGAATAAAAAATCAAGAATTGACAA
* *
47571076 TTGAGAATAAAACATCAAGAA
1 TTTAGAATAAAAAATCAAGAA
47571097 CAAACAATTG
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (28 bp):
TTTAGAATAAAAAATCAAGAATTGACAA
Found at i:47571123 original size:28 final size:29
Alignment explanation
Indices: 47571072--47571129 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
47571062 TCGAGAATTG
*
47571072 ACAATTGAGAATAAAACATCAAGAA-CAA
1 ACAATTGAGAACAAAACATCAAGAATCAA
*
47571100 ACAATTGAGAACAAGAA-ATTAAGAATCAA
1 ACAATTGAGAACAA-AACATCAAGAATCAA
47571129 A
1 A
47571130 TTGTGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (29 bp):
ACAATTGAGAACAAAACATCAAGAATCAA
Found at i:47572752 original size:30 final size:30
Alignment explanation
Indices: 47572716--47572781 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
47572706 TTGAAAAGAG
47572716 TTAGAAAGTTTTAAAGCAAACTAACAATTT
1 TTAGAAAGTTTTAAAGCAAACTAACAATTT
47572746 TTAGAAAGTTTTAAAGCAAACTAACAATTT
1 TTAGAAAGTTTTAAAGCAAACTAACAATTT
47572776 TT-GAAA
1 TTAGAAA
47572782 CAGGGGTCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 4 0.11
30 32 0.89
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (30 bp):
TTAGAAAGTTTTAAAGCAAACTAACAATTT
Found at i:47574006 original size:75 final size:76
Alignment explanation
Indices: 47573911--47574095 Score: 232
Period size: 76 Copynumber: 2.4 Consensus size: 76
47573901 GCGCCCAGCA
* *
47573911 CTAGTCGGATAAATAAAAGGTATCAAATGTGTGC-TAGCACCAGTCGGATAAAC-CAACAATGAG
1 CTAGTCGGATAAATCAAAGGTATCAAATGTGTGCTTAGCACCAATCGGATAAACTCAA-AATGAG
47573974 TTGCACCCAACG
65 TTGCACCCAACG
* * * * * *
47573986 TTAGTCTGATAAATCGAAGGTATCAAATGTGTGCTTAGCACTAATTGGATAAACTGAAAATGAGT
1 CTAGTCGGATAAATCAAAGGTATCAAATGTGTGCTTAGCACCAATCGGATAAACTCAAAATGAGT
47574051 TGCACCCAACG
66 TGCACCCAACG
* * *
47574062 CTAGTCGGATAGA-CTAACGATATCAAATGTGTGC
1 CTAGTCGGATAAATC-AAAGGTATCAAATGTGTGC
47574096 CTGTCATTGT
Statistics
Matches: 93, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
75 31 0.33
76 60 0.65
77 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (76 bp):
CTAGTCGGATAAATCAAAGGTATCAAATGTGTGCTTAGCACCAATCGGATAAACTCAAAATGAGT
TGCACCCAACG
Found at i:47588697 original size:17 final size:18
Alignment explanation
Indices: 47588657--47588698 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
47588647 CCATTATGTT
47588657 ATTAAATAGACATTTAAA
1 ATTAAATAGACATTTAAA
* *
47588675 AATAAATATA-ATTTAAA
1 ATTAAATAGACATTTAAA
*
47588692 TTTAAAT
1 ATTAAAT
47588699 TATTAGTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
ATTAAATAGACATTTAAA
Found at i:47594580 original size:68 final size:68
Alignment explanation
Indices: 47594413--47594588 Score: 150
Period size: 68 Copynumber: 2.6 Consensus size: 68
47594403 TAGTACCACT
* * * * *
47594413 CATGCGACCTAGC--CA-ATTTGTCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCTACATATATATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAAT
*
47594475 CACG
65 CACA
* * *
47594479 CATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGT
1 CATGCGACCTAGCTACATATATATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGA
47594541 ATCACA
63 ATCACA
*
47594547 CATGTGACCTAGCTACTATATAGTATCTCGTAGC-CTTCTTGT
1 CATGCGACCTAGCTAC-ATATA-TATCTCGTAGCTC-TCTTGT
47594589 ACACATGATG
Statistics
Matches: 90, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
66 13 0.14
67 1 0.01
68 35 0.39
69 9 0.10
70 6 0.07
71 26 0.29
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (68 bp):
CATGCGACCTAGCTACATATATATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATC
ACA
Found at i:47598770 original size:27 final size:27
Alignment explanation
Indices: 47598716--47598779 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
47598706 ATTCTTTAGC
47598716 ATTTTTATAATTTTTTTAAAAATAT-AA
1 ATTTTTA-AATTTTTTTAAAAATATAAA
* * *
47598743 ATTTTTAAATTTTTATTAATATTTTAAA
1 ATTTTTAAATTTTT-TTAAAAATATAAA
47598771 ATTTTTAAA
1 ATTTTTAAA
47598780 ATTTGTTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 7 0.22
27 14 0.44
28 11 0.34
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTTTAAATTTTTTTAAAAATATAAA
Found at i:47602521 original size:43 final size:42
Alignment explanation
Indices: 47602417--47602536 Score: 134
Period size: 43 Copynumber: 2.8 Consensus size: 42
47602407 AGGGTTACTA
* * *
47602417 AGATTACGTGTAAGACCATATCTGGGATATGGCATCGATATG
1 AGATTACGTGTAAGACCATAGCTAGGATATGGCATCGATACG
* *
47602459 AGACTT-CGTCTAAGACCATAGCTAGGCTATTGGCATCGATACG
1 AGA-TTACGTGTAAGACCATAGCTAGGATA-TGGCATCGATACG
* * * *
47602502 AGATTACATGTAAGTCCATATCTGGGATATGGCAT
1 AGATTACGTGTAAGACCATAGCTAGGATATGGCAT
47602537 TAGTACGGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 30 0.47
43 34 0.53
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28
Consensus pattern (42 bp):
AGATTACGTGTAAGACCATAGCTAGGATATGGCATCGATACG
Found at i:47605724 original size:21 final size:21
Alignment explanation
Indices: 47605698--47605748 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
47605688 TCAACACATG
*
47605698 GGCGTGTGGGATGGCCAAACT
1 GGCGTGTGGGATGCCCAAACT
*
47605719 GGCGTGTGGGATGCCCACACT
1 GGCGTGTGGGATGCCCAAACT
47605740 GGCGTGTGG
1 GGCGTGTGG
47605749 ATTAGCCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.14, C:0.22, G:0.45, T:0.20
Consensus pattern (21 bp):
GGCGTGTGGGATGCCCAAACT
Found at i:47611193 original size:14 final size:14
Alignment explanation
Indices: 47611174--47611201 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47611164 AGAATATATT
47611174 TTTAATTAATTAAA
1 TTTAATTAATTAAA
47611188 TTTAATTAATTAAA
1 TTTAATTAATTAAA
47611202 AATTTTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:47622712 original size:17 final size:17
Alignment explanation
Indices: 47622690--47622723 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
47622680 GGTATAAGGC
47622690 GCATCTTGTAGCTAAAG
1 GCATCTTGTAGCTAAAG
47622707 GCATCTTGTAGCTAAAG
1 GCATCTTGTAGCTAAAG
47622724 TATATACTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (17 bp):
GCATCTTGTAGCTAAAG
Done.